<tifffile.TiffFile '20240823-CRC-TMA…_a4_ac.ome.tiff'> OME series cannot handle discontiguous storage ((1200, 1) != (1200, 1200))

[MayXiaoqingChen]

Hello,

I have been running through the imc_preprocessing.py and I keep getting this error:
<tifffile.TiffFile '20240823-CRC-TMA…_a4_ac.ome.tiff'> OME series cannot handle discontiguous storage ((1200, 1) != (1200, 1200))

I have updated my tifffile module but that didn't resolve anything. When I look at my ome.tiff file it is very small (1x1200 pixels) which doesn't seem right, but the mcd file from which it is converted seems normal. All my ome.tiffs have converted into 1x1200.

I was wondering if anyone has run into this error before and has some advice

[liangyuli12138]

Hi, I met the same problem. Could you tell me how to solve this problem.

[MayXiaoqingChen]

Hi, I met the same problem. Could you tell me how to solve this problem.

The error arises because the version of the tifffile module is incorrect. In the author's example(https://github.com/BodenmillerGroup/ImcSegmentationPipeline/blob/main/scripts/imc_preprocessing.ipynb), the version of the tifffile module is 2023.4.12 (See the bottom of the linked page), while my version is 2024.8.30.
So we need to uninstall the tifffile module and return to the old version of the tifffile module:
pip uninstall tifffile
pip install tifffile==2023.4.12

The above solution resolved my problem.

[votti]

BodenmillerGroup/xtiff#25

Is the underlying reason for this that needs to be fixed @Milad4849